Overview

We manually curated 500\(+\) multiple modality PPMI MRI subjects. 5 messages from this effort.

  1. Raw data quality is overall high
  1. Processing improves quality/usability further
  1. Detailed curation results provide a unique resource in itself

  1. Enables investigation of the “meaning” of M3RI at the individual level

  2. Empowers investigation of the “meaning” of M3RI at the population level

the PPMI500 cohort

Table 1. Baseline cohort for subjects with T1w IDPs and non-missing diagnosis.
CN GenAR LRRK2PD SporadicAR SporadicPD p
(N=47) (N=1) (N=4) (N=230) (N=217)
age 63.5 ± 12.5 71.9 ± NA 59.3 ± 7.1 67.7 ± 5.7 64.5 ± 9.4 < 0.001
Sex 0.026
    Female 23 (48.9%) 1 (100.0%) 3 (75.0%) 102 (44.3%) 72 (33.2%)
    Male 24 (51.1%) 0 ( 0.0%) 1 (25.0%) 128 (55.7%) 145 (66.8%)
duration.yrs         2.1 ± 0.7     1.0 ± 0.7 0.002
updrs.totscore 5.3 ± 3.8 14.0 ± NA 30.3 ± 13.1 12.1 ± 9.3 36.5 ± 15.0 < 0.001
CSFSAA < 0.001
    Negative 36 (85.7%) 1 (100.0%) 2 (50.0%) 82 (38.7%) 10 ( 4.9%)
    Positive 6 (14.3%) 0 ( 0.0%) 2 (50.0%) 130 (61.3%) 194 (95.1%)
LEDD 0.0 ± 0.0 0.0 ± NA 259.0 ± 317.7 1.3 ± 19.8 3.6 ± 30.3 < 0.001
hasDTI 0.117
    FALSE 9 (19.1%) 1 (100.0%) 1 (25.0%) 57 (24.8%) 38 (17.5%)
    TRUE 38 (80.9%) 0 ( 0.0%) 3 (75.0%) 173 (75.2%) 179 (82.5%)
hasfMRI 0.003
    FALSE 5 (10.6%) 1 (100.0%) 0 ( 0.0%) 12 ( 5.2%) 15 ( 6.9%)
    TRUE 42 (89.4%) 0 ( 0.0%) 4 (100.0%) 218 (94.8%) 202 (93.1%)

1. Data quality is overall high

How do we define M3RI quality?

  • we manually QC’d each modality for each of 500 baseline subjects

    • characterize reasons for failure

what is the QC protocol?

  • Review QC protocol – generally speaking

what are the QC results?

  • Summarize QC results for each modality

    • raw data QC and failure rates

  • Summarize results for “joint” quality - how many subjects are high quality across all modalities at once?

Tables of Manual QC results

Table 2 Patterns of QC results by modality: FLAIR
T2Flair p
(N=549)
qcfail_orientation
    True 1 (100.0%)
qcfail_intensity_saturation
    True 4 (100.0%)
qcfail_background_noise
    True 6 (100.0%)
qcfail_motion
    True 10 (100.0%)
qcfail_other
    True 2 (100.0%)
qchuman_FLAIR < 0.001
    False 25 ( 4.6%)
    True 524 (95.4%)
has_humanqc
    1 549 (100.0%)
Table 3 Patterns of QC results by modality: T1w
T1w p
(N=523)
qcfail_background_noise
    True 2 (100.0%)
qcfail_motion
    True 4 (100.0%)
qcfail_other
    True 4 (100.0%)
qchuman_T1w < 0.001
    False 10 ( 1.9%)
    True 513 (98.1%)
has_humanqc
    1 523 (100.0%)
Table 4 Patterns of QC results by modality: NM
Neuromelanin p
(N=502)
NM_QC_Ratings_Z < 0.001
    0 88 (18.3%)
    1 393 (81.7%)
NM_QC_Ratings_SNVol < 0.001
    0 7 ( 1.5%)
    1 474 (98.5%)
NM_QC_Ratings_AvgIntensity < 0.001
    0 5 ( 1.0%)
    1 473 (99.0%)
NM_QC_Ratings_SDIntensity < 0.001
    0 5 ( 1.0%)
    1 473 (99.0%)
NM_QC_Ratings_MaxIntensity < 0.001
    0 5 ( 1.0%)
    1 473 (99.0%)
NM_QC_Ratings_Failures < 0.001
    0 386 (80.8%)
    1 81 (16.9%)
    2 6 ( 1.3%)
    3 4 ( 0.8%)
    4 1 ( 0.2%)
Table 5 Patterns of QC results by modality: DTI
DTIb0 DTIdwi p
(N=1204) (N=1340)
qcfail_orientation
    True 16 (100.0%) 16 (100.0%)
qcfail_phantom
    True 6 (100.0%) 6 (100.0%)
qcfail_intensity_saturation
    True 0 ( 0.0%) 4 (100.0%)
qcfail_background_noise
    True 50 (100.0%) 54 (100.0%)
qcfail_motion
    True 54 (100.0%) 70 (100.0%)
qcfail_signal_dropout
    True 14 (100.0%) 22 (100.0%)
qcfail_other 1.000
    GHOSTING 10 (62.5%) 10 (62.5%)
    True 6 (37.5%) 6 (37.5%)
qchuman_DTI 0.481
    False 94 ( 7.8%) 116 ( 8.7%)
    True 1110 (92.2%) 1224 (91.3%)
has_humanqc
    1 1204 (100.0%) 1340 (100.0%)
Table 6 Patterns of QC results by modality: rsfMRI
rsfMRI rsfMRI_LR rsfMRI_RL p
(N=2969) (N=187) (N=854)
qcfail_orientation
    True 9 (100.0%) 1 (100.0%) 16 (100.0%)
qcfail_phantom
    True 14 (100.0%) 0 ( 0.0%) 0 ( 0.0%)
qcfail_spacing
    True 14 (100.0%) 0 ( 0.0%) 0 ( 0.0%)
qcfail_intensity_saturation
    True 20 (100.0%) 10 (100.0%) 32 (100.0%)
qcfail_motion
    True 581 (100.0%) 0 ( 0.0%) 0 ( 0.0%)
qcfail_signal_dropout
    True 165 (100.0%) 15 (100.0%) 48 (100.0%)
qcfail_temporal_noise
    True 1 (100.0%) 1 (100.0%) 8 (100.0%)
qcfail_insufficient_volumes
    True 12 (100.0%) 0 ( 0.0%) 0 ( 0.0%)
qcfail_FOV
    True 1 (100.0%) 0 ( 0.0%) 0 ( 0.0%)
qcfail_other < 0.001
    472 volumes, restart appended to initial scan? 0 ( 0.0%) 0 ( 0.0%) 8 (33.3%)
    axial slices look wrong way around? 0 ( 0.0%) 1 (50.0%) 8 (33.3%)
    strange artifacts in tsnr 0 ( 0.0%) 1 (50.0%) 8 (33.3%)
    True 1 (50.0%) 0 ( 0.0%) 0 ( 0.0%)
    wrap-around artifact 1 (50.0%) 0 ( 0.0%) 0 ( 0.0%)
qchuman_rsfMRI 0.002
    False 457 (15.4%) 19 (10.2%) 96 (11.2%)
    True 2512 (84.6%) 168 (89.8%) 758 (88.8%)
has_humanqc
    1 2969 (100.0%) 187 (100.0%) 854 (100.0%)

T1w results

T1w QC summary
modality Total Successes Failures Percent_Success Percent_Failure failcat
T1w 523 513 10 98.08795 1.9120459 qchuman_T1w
T1w 523 521 2 99.61759 0.3824092 qcfail_background_noise
T1w 523 519 4 99.23518 0.7648184 qcfail_motion
T1w 523 519 4 99.23518 0.7648184 qcfail_other

Flair results

FLAIR QC summary
modality Total Successes Failures Percent_Success Percent_Failure failcat
T2Flair 549 524 25 95.44627 4.5537341 qchuman_FLAIR
T2Flair 549 548 1 99.81785 0.1821494 qcfail_orientation
T2Flair 549 545 4 99.27140 0.7285974 qcfail_intensity_saturation
T2Flair 549 543 6 98.90710 1.0928962 qcfail_background_noise
T2Flair 549 539 10 98.17851 1.8214936 qcfail_motion
T2Flair 549 547 2 99.63570 0.3642987 qcfail_other

DT results

DTI QC summary
modality Total Successes Failures Percent_Success Percent_Failure failcat
DTIb0 1204 1110 94 92.19269 7.8073090 qchuman_DTI
DTIdwi 1340 1224 116 91.34328 8.6567164 qchuman_DTI
DTIb0 1204 1188 16 98.67110 1.3289037 qcfail_orientation
DTIdwi 1340 1324 16 98.80597 1.1940299 qcfail_orientation
DTIb0 1204 1198 6 99.50166 0.4983389 qcfail_phantom
DTIdwi 1340 1334 6 99.55224 0.4477612 qcfail_phantom
DTIb0 1204 1204 0 100.00000 0.0000000 qcfail_intensity_saturation
DTIdwi 1340 1336 4 99.70149 0.2985075 qcfail_intensity_saturation
DTIb0 1204 1154 50 95.84718 4.1528239 qcfail_background_noise
DTIdwi 1340 1286 54 95.97015 4.0298507 qcfail_background_noise
DTIb0 1204 1150 54 95.51495 4.4850498 qcfail_motion
DTIdwi 1340 1270 70 94.77612 5.2238806 qcfail_motion
DTIb0 1204 1190 14 98.83721 1.1627907 qcfail_signal_dropout
DTIdwi 1340 1318 22 98.35821 1.6417910 qcfail_signal_dropout
DTIb0 1204 1188 16 98.67110 1.3289037 qcfail_other
DTIdwi 1340 1324 16 98.80597 1.1940299 qcfail_other

rsfMRI results

rsfMRI QC summary
modality Total Successes Failures Percent_Success Percent_Failure failcat
rsfMRI 2969 2512 457 84.60761 15.3923880 qchuman_rsfMRI
rsfMRI_LR 187 168 19 89.83957 10.1604278 qchuman_rsfMRI
rsfMRI_RL 854 758 96 88.75878 11.2412178 qchuman_rsfMRI
rsfMRI 2969 2960 9 99.69687 0.3031324 qcfail_orientation
rsfMRI_LR 187 186 1 99.46524 0.5347594 qcfail_orientation
rsfMRI_RL 854 838 16 98.12646 1.8735363 qcfail_orientation
rsfMRI 2969 2955 14 99.52846 0.4715392 qcfail_phantom
rsfMRI_LR 187 187 0 100.00000 0.0000000 qcfail_phantom
rsfMRI_RL 854 854 0 100.00000 0.0000000 qcfail_phantom
rsfMRI 2969 2955 14 99.52846 0.4715392 qcfail_spacing
rsfMRI_LR 187 187 0 100.00000 0.0000000 qcfail_spacing
rsfMRI_RL 854 854 0 100.00000 0.0000000 qcfail_spacing
rsfMRI 2969 2949 20 99.32637 0.6736275 qcfail_intensity_saturation
rsfMRI_LR 187 177 10 94.65241 5.3475936 qcfail_intensity_saturation
rsfMRI_RL 854 822 32 96.25293 3.7470726 qcfail_intensity_saturation
rsfMRI 2969 2388 581 80.43112 19.5688784 qcfail_motion
rsfMRI_LR 187 187 0 100.00000 0.0000000 qcfail_motion
rsfMRI_RL 854 854 0 100.00000 0.0000000 qcfail_motion
rsfMRI 2969 2804 165 94.44257 5.5574267 qcfail_signal_dropout
rsfMRI_LR 187 172 15 91.97861 8.0213904 qcfail_signal_dropout
rsfMRI_RL 854 806 48 94.37939 5.6206089 qcfail_signal_dropout
rsfMRI 2969 2968 1 99.96632 0.0336814 qcfail_temporal_noise
rsfMRI_LR 187 186 1 99.46524 0.5347594 qcfail_temporal_noise
rsfMRI_RL 854 846 8 99.06323 0.9367681 qcfail_temporal_noise
rsfMRI 2969 2957 12 99.59582 0.4041765 qcfail_insufficient_volumes
rsfMRI_LR 187 187 0 100.00000 0.0000000 qcfail_insufficient_volumes
rsfMRI_RL 854 854 0 100.00000 0.0000000 qcfail_insufficient_volumes
rsfMRI 2969 2968 1 99.96632 0.0336814 qcfail_FOV
rsfMRI_LR 187 187 0 100.00000 0.0000000 qcfail_FOV
rsfMRI_RL 854 854 0 100.00000 0.0000000 qcfail_FOV

NM results

NM QC summary
NM.QC.cat Total Successes Failures Percent_Success Percent_Failure failcat
overall 478 386 92 80.75314 19.246862 NM_QC_Ratings_Failures
z.coord 478 391 87 81.79916 18.200837 NM_QC_Ratings_Z
sn.vol 478 471 7 98.53556 1.464435 NM_QC_Ratings_SNVol
avg.int 478 473 5 98.95397 1.046025 NM_QC_Ratings_AvgIntensity
sd.int 478 473 5 98.95397 1.046025 NM_QC_Ratings_SDIntensity
max.int 478 473 5 98.95397 1.046025 NM_QC_Ratings_MaxIntensity 
## Warning in merge.data.frame(temp, temp2, by = "dtid2", all.x = TRUE): column
## names 'qchuman_DTI.x', 'qchuman_DTI.y' are duplicated in the result
## Warning in merge.data.frame(temp, temp2, by = "rsfid1", all.x = TRUE): column
## names 'qchuman_DTI.x', 'qchuman_DTI.y' are duplicated in the result
## Warning in merge.data.frame(temp, temp2, by = "rsfid2", all.x = TRUE): column
## names 'qchuman_DTI.x', 'qchuman_DTI.y', 'qchuman_rsfMRI.x', 'qchuman_rsfMRI.y'
## are duplicated in the result

do a check based on rsfmri motion – if the qc data “makes sense”

do a check based on DTI – if the qc data “makes sense”

do a check based on NM – if the qc data “makes sense”

do a check based on FLAIR – if the qc data “makes sense”

do a check based on T1w – if the qc data “makes sense”

2. Detailed curation results provide a unique resource in itself

for algorithm developers

  • we ourselves benefit from this (will show examples)

for scientists

  • to have confidence (or at least context regarding quality) in looking at automated IDPs derived from these data

3. Processing improves quality/usability further

effect of processing by modality

  • for each, summarize how processing improves the data

    • rsfMRI is “easy” to see - throw away motion corrupted data

    • developed methodology specific for PPMI that was informed by this process

    • automated QC for these modalities for future work

we provide scientists handles on this so that can be “strict” or “loose” in data selection

  • we document these parameters

4. Enables investigation of the “meaning” of M3RI at the individual level

5. Empowers investigation of the “meaning” of M3RI at the population level